The World Government could be the captors. They might see Marco as a threat due to his power and his connection to the late Whitebeard. They could want to study his phoenix abilities or keep him locked away to prevent any uprisings.
It could be the Blackbeard Pirates. Since they have a history with the Whitebeard Pirates, they might capture Marco to get information or as a form of revenge.
Well, he might be used as a bargaining chip against the Whitebeard Pirates. His captors could try to extract information about the pirates' secrets or hidden treasures.
Perhaps Marco uses his intelligence to outwit his captors. He could pretend to be weak or injured and when they least expect it, he could make his move. He has a lot of experience from his time with Whitebeard, so he could use that knowledge to find a weakness in their security and escape.
There's a possibility that it's a villainous trainer. This trainer might capture Gengar with the intention of using it for evil purposes, like using Gengar's powers to steal other Pokémon or cause chaos in Pokémon battles.
Maybe it's an old foe who has managed to regain power and wants to make Sora pay for past defeats. For example, a powerful dark sorcerer who was once defeated by Sora but has now found a way to capture him through some devious plot.
It could be Captain Hook. He has always been Peter Pan's nemesis and has a strong motive to capture him. Maybe he wants to finally get revenge for all the times Peter has outsmarted him.
It could be Discord. He loves causing chaos and might capture Twilight Sparkle just for the fun of it or to disrupt the harmony in Equestria.
Another possibility is that a rival pirate group that has a long - standing feud with the Whitebeard Pirates managed to finally get the upper hand and capture Marco. They could have been studying his movements for a long time and found a weakness in his defenses. This group might be led by a very cunning and powerful pirate captain who has a personal vendetta against the Whitebeard Pirates and sees capturing Marco as a major victory.
Another possibility is a group of corrupted Plumbers. They turn against Ben and capture him, perhaps because they want to use the Omnitrix for their own evil purposes. They would have knowledge of Ben's abilities and how to contain him, which would make for an interesting conflict.
It could be Team Rocket. They've always been after Ash and his Pikachu. They might finally succeed in capturing him and then Pikachu has to come up with a plan to rescue Ash.
Maybe some mad scientist who wants to experiment on Beast Boy's shape - shifting DNA. He could be looking for a way to transfer the ability to himself or create some sort of mutant army. Another option is that it's a group of aliens who mistake Beast Boy for a dangerous creature and capture him to study. They might not understand that he's a sentient being with friends who will come looking for him.